Effects of high medium pH on growth, metabolism and transport in Saccharomyces cerevisiae

Yeast-based assay to identify inhibitors of the malaria parasite sodium phosphate uptake transporter as potential novel antimalarial drugs

Malaria affects almost 250 million people annually and continues to be a significant threat to global public health. Infection with protozoan parasites from the genus Plasmodium causes malaria. The primary treatment for malaria is artemisinin-based combination therapies (ACTs). The spread of ACT-resistant parasites has undermined efforts to control and eradicate malaria. Thus, it is crucial to identify new targets for the development of novel antimalarial drugs. Phosphate is an essential nutrient for all cells. The Plasmodium falciparum genome encodes a single sodium-coupled inorganic phosphate transporter named PfPiT that is essential for parasite proliferation in the asexual blood stage. Thus, PfPiT inhibitors may be promising antimalarial drugs. Like Plasmodium, yeast requires phosphate to grow. We developed a Saccharomyces cerevisiae based growth assay to identify inhibitors of PfPiT. Genome editing was used to create a yeast strain where PfPiT was the only phosphate transporter. Using a radioactive [32P]phosphate uptake assay, the measured phosphate Km for PfPiT in yeast was 56 ± 7 μM in 1 mM NaCl at pH 7.4. The Km decreased to 24 ± 3 μM in 25 mM NaCl consistent with it being a Na+ coupled cotransporter. Conditions under which yeast growth was dependent on phosphate uptake mediated by PfPiT were identified and a 22-h growth assay was developed to screen for PfPiT inhibitors. In a screen of 21 compounds, two compounds were identified that inhibited the growth of the PfPiT strain but not that of the parental strain expressing Pho84, one of the five endogenous yeast phosphate transporters. Radioactive phosphate uptake experiments confirmed inhibition of phosphate uptake by the two compounds. The growth inhibition assay provides a simple and inexpensive approach to screen a large compound library for PfPiT inhibitors that may serve as starting points for the development of novel antimalarial drugs.

Engineering Saccharomyces cerevisiae for the production of natural osmolyte glucosyl glycerol from sucrose and glycerol through Ccw12-based surface display of sucrose phosphorylase

BACKGROUND

Yeast Saccharomyces cerevisiae is widely recognised as a versatile chassis for constructing microbial cell factories. However, producing chemicals from toxic, highly concentrated, or cell-impermeable substrates, or chemicals dependent on enzymatic reactions incompatible with the yeast's intracellular environment, remains challenging. One such chemical is 2-O-(α-D-glucopyranosyl)-sn-glycerol (glucosyl glycerol, αGG), a natural osmolyte used in the cosmetics and healthcare industries. This compound can be synthesised in a one-enzyme reaction from sucrose and glycerol by Leuconostoc mesenteroides sucrose phosphorylase (SucP), an enzyme which, in a low-water, glycerol-rich, phosphate-free environment, transfers the glucosyl moiety from sucrose to glycerol.

RESULTS

In this study, we engineered a yeast microbial cell factory for αGG production. For this purpose, we first focused on the abundant yeast GPI-anchored cell wall protein Ccw12 and used our insights to develop a miniature Ccw12-tag, which adds only 1.1 kDa to the enzyme of interest while enabling its covalent attachment to the cell wall. Next, we Ccw12-tagged SucP and expressed it in an invertase-negative strain of yeast S. cerevisiae from the PHO5 promoter, i.e., promoter strongly induced under phosphate-free conditions. Such SucP isoform, covalently C-terminally anchored to the outer cell surface, produced extracellularly 37.3 g l- 1 (146 mM) of αGG in five days, while the underlying chassis metabolised reaction by-products, thereby simplifying downstream processing.

CONCLUSIONS

The here-described S. cerevisiae strain, displaying C-terminally anchored sucrose phosphorylase on its cell surface, is the first eukaryotic microbial cell factory capable of a one-step αGG production from the readily available substrates sucrose and glycerol.

Assessing Process Conditions on Xylose Fermentation in Spathaspora passalidarum: Effects of pH, Substrate-to-Inoculum Ratio, Temperature, and Initial Ethanol Concentration

Bioethanol represents a clean and renewable alternative to fossil fuels, offering a significant reduction in environmental impact. Second-generation ethanol (2G) is produced using lignocellulosic biomass, which presents additional challenges due to the presence of hemicellulose. The pentose sugars within hemicellulose cannot be efficiently metabolized by conventional yeast strains like Saccharomyces cerevisiae. Consequently, the yeast Spathaspora passalidarum has emerged as a promising candidate for mixed fermentation processes, given its ability to utilize xylose. This study presents an in-depth metabolic, stoichiometric, and kinetic analysis of the fermentation performance of Sp. passalidarum NRRL Y-27907 in mixed glucose and xylose cultures. Emphasis was placed on examining variables from a novel perspective compared to existing literature. Specifically, the impacts of initial inoculum-substrate ratios, substrate composition, pH, temperature, and ethanol sensitivity were analyzed using a mathematical bioprocess approach. Sp. passalidarum NRRL Y-27907 exhibited sequential sugar consumption, with xylose being utilized only after glucose was exhausted. Ethanol yields in mixed cultures were comparable to those in individual-sugar cultures. The best fermentative performance was observed at 30 °C, with 25 g/L of xylose and an inoculum of 0.50 g/L. The strain exhibited significant robustness at pH 4.0 and was notably affected by initial ethanol concentrations up to 20 g/L. These findings provide crucial insights into the metabolic and fermentative behavior of Sp. passalidarum NRRL Y-27907, offering valuable information for the design of consolidated bioprocesses from lignocellulosic materials.

The evaluation of Starmerella magnoliae X3 as a biodiesel feedstock based on triacylglycerol (TAG) production, lipid productivity, and fatty acid profile under nitrogen limitation and acidic pH conditions

The effects of four initial culture pH values (3, 4, 5, and 6) and nitrogen limitation on growth, TAG accumulation, lipid production, fatty acid profile, and estimated biodiesel quality of Starmerella magnoliae X3 were investigated. TAG and lipid levels were measured by Nile Red fluorescence and sulfo-phospho-vanilin (SPV) techniques, respectively. The results showed that a combination of nitrogen limitation and acidic pH significantly (p < 0.05) increased TAG accumulation, total lipid contents, and lipid productivity in Starmerella magnoliae X3 compared to the control group. Under nitrogen limitation, the highest TAG accumulation was achieved at initial pHs of 3 and 5 after 72 h of cultivation, and the highest lipid productivity (0.306 g L-1 d-1) was observed after 48 h at pH 3; the major fatty acids at the four pH values were oleic acid (63.6%-64%), palmitoleic acid (11.3%-12.5%), stearic acid (9.7%-11.4%), and palmitic acid (9.4%-10%). In addition, both stresses were associated with lower iodine value and higher cetane number of the biodiesel compared to the control. These findings suggest that cultivation in a low-nitrogen medium at an initial pH of 3 or 5 holds promise in increasing TAG production in Starmerella magnoliae X3.

Transient hypoxia drives soil microbial community dynamics and biogeochemistry during human decomposition

Human decomposition in terrestrial ecosystems is a dynamic process creating localized hot spots of soil microbial activity. Longer-term (beyond a few months) impacts on decomposer microbial communities are poorly characterized and do not typically connect microbial communities to biogeochemistry, limiting our understanding of decomposer communities and their functions. We performed separate year-long human decomposition trials, one starting in spring, another in winter, integrating bacterial and fungal community structure and abundances with soil physicochemistry and biogeochemistry to identify key drivers of microbial community change. In both trials, soil acidification, elevated microbial respiration, and reduced soil oxygen concentrations occurred. Changes in soil oxygen concentrations were the primary driver of microbial succession and nitrogen transformation patterns, while fungal community diversity and abundance was related to soil pH. Relative abundance of facultative anaerobic taxa (Firmicutes and Saccharomycetes) increased during the period of reduced soil oxygen. The magnitude and timing of the decomposition responses were amplified during the spring trial relative to the winter, even when corrected for thermal inputs (accumulated degree days). Further, soil chemical parameters, microbial community structure, and fungal gene abundances remained altered at the end of 1 year, suggesting longer-term impacts on soil ecosystems beyond the initial pulse of decomposition products.

Initial acidic media promotes quiescence entry in Saccharomyces cerevisiae

Quiescence is a conserved cellular state wherein cells cease proliferation and remain poised to re-enter the cell cycle when conditions are appropriate. Budding yeast is a powerful model for studying cellular quiescence. In this work, we demonstrate that the pH of the YPD media strongly affects quiescence entry efficiency in Saccharomyces cerevisiae. Adjusting the initial media pH to 5.5 significantly improves quiescence entry efficiency compared to unadjusted YPD media. Thermotolerance of the produced quiescence yeast are similar, suggesting the media pH influences the quantity of quiescent cells more than quality of quiescence reached.

Acidic media promotes quiescence entry in Saccharomyces cerevisiae

Quiescence is a conserved cellular state wherein cells cease proliferation and remain poised to re-enter the cell cycle when conditions are appropriate. Budding yeast is a powerful model for studying cellular quiescence. In this work, we demonstrate that the pH of the YPD media strongly affects quiescence entry efficiency in Saccharomyces cerevisiae. Adjusting media pH to 5.5 significantly improves quiescence entry efficiency compared to unadjusted YPD media. Thermotolerance of the produced quiescence yeast are similar, suggesting the media pH influences the quantity of quiescent cells more than quality of quiescence reached.

Quantitative assessment of cardiomyocyte mechanobiology through high-throughput cantilever-based functional well plate systems

Proper regulation of the in vitro cell culture environment is essential for disease modelling and drug toxicity screening. The main limitation of well plates used for cell culture is that they cannot accurately maintain energy sources and compounds needed during cell growth. Herein, to understand the importance of perfusion in cardiomyocyte culture, changes in contractile force and heart rate during cardiomyocyte growth are systematically investigated, and the results are compared with those of a perfusion-free system. The proposed perfusion system consists of a Peltier refrigerator, a peristaltic pump, and a functional well plate. A functional well plate with 12 wells is made through injection moulding, with two tubes integrated in the cover for each well to continuously circulate the culture medium. The contractile force of cardiomyocytes growing on the cantilever surface is analysed through changes in cantilever displacement. The maturation of cardiomyocytes is evaluated through fluorescence staining and western blot; cardiomyocytes cultured in the perfusion system show greater maturity than those cultured in a manually replaced culture medium. The pH of the culture medium manually replaced at intervals of 3 days decreases to 6.8, resulting in an abnormal heartbeat, while cardiomyocytes cultured in the perfusion system maintained at pH 7.4 show improved contractility and a uniform heart rate. Two well-known ion channel blockers, verapamil and quinidine, are used to measure changes in the contractile force of cardiomyocytes from the two systems. Cardiomyocytes in the perfusion system show greater stability during drug toxicity screening, proving that the perfusion system provides a better environment for cell growth.

New insights into Saccharomyces cerevisiae induced calcium carbonate precipitation

Our previous study reported that Saccharomyces cerevisiae could induce calcium carbonate (CaCO3) precipitation, but the associated mechanism was unclear. In the present study, Saccharomyces cerevisiae was cultured under various conditions, including the presence of different organic acids and initial pH, and the yields of CaCO3 formation induced by the different organic acids were compared. The metabolism of organic acid by the metabolites of S. cerevisiae was also assessed in vitro. The SEM-EDS and XRD results showed that only acetate acid, pyruvic acid, and α-ketoglutaric acid could induce CaCO3 formation, and the weight order of the produced CaCO3 was pyruvic acid, acetate acid, α-ketoglutaric acid. In addition, the presence of only yeast metabolites and the initial neutral or alkaline environment also limited the CaCO3 formation. These results illustrated that organic acid oxidation intracellularly, especially the tricarboxylic acid cycle, was the major mechanism, and the CaCO3 yield was related to the amount of CO2 produced by the metabolism of organic acids. These findings will deepen the knowledge of the mineralization capacity of S. cerevisiae and provide a theoretical basis for the future application of yeast as an alternative microorganism in MICP.

Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches

Optimizing the production of recombinant proteins is a problem of major industrial and pharmaceutical importance. Secretion of the protein by the host cell considerably simplifies downstream purification processes. However, for many proteins, this is also the limiting production step. Current solutions involve extensive engineering of the chassis cell to facilitate protein trafficking and limit protein degradation triggered by excessive secretion-associated stress. Here, we propose instead a regulation-based strategy in which induction is dynamically adjusted to an optimal strength based on the current stress level of the cells. Using a small collection of hard-to-secrete proteins, a bioreactor-based platform with automated cytometry measurements, and a systematic assay to quantify secreted protein levels, we demonstrate that the secretion sweet spot is indicated by the appearance of a subpopulation of cells that accumulate high amounts of proteins, decrease growth, and face significant stress, that is, experience a secretion burnout. In these cells, adaptations capabilities are overwhelmed by a too strong production. Using these notions, we show for a single-chain antibody variable fragment that secretion levels can be improved by 70% by dynamically keeping the cell population at optimal stress levels using real-time closed-loop control.

Structural characterization of the Aspergillus niger citrate transporter CexA uncovers the role of key residues S75, R192 and Q196

The Aspergillus niger CexA transporter belongs to the DHA1 (Drug-H+ antiporter) family. CexA homologs are exclusively found in eukaryotic genomes, and CexA is the sole citrate exporter to have been functionally characterized in this family so far. In the present work, we expressed CexA in Saccharomyces cerevisiae, demonstrating its ability to bind isocitric acid, and import citrate at pH 5.5 with low affinity. Citrate uptake was independent of the proton motive force and compatible with a facilitated diffusion mechanism. To unravel the structural features of this transporter, we then targeted 21 CexA residues for site-directed mutagenesis. Residues were identified by a combination of amino acid residue conservation among the DHA1 family, 3D structure prediction, and substrate molecular docking analysis. S. cerevisiae cells expressing this library of CexA mutant alleles were evaluated for their capacity to grow on carboxylic acid-containing media and transport of radiolabeled citrate. We also determined protein subcellular localization by GFP tagging, with seven amino acid substitutions affecting CexA protein expression at the plasma membrane. The substitutions P200A, Y307A, S315A, and R461A displayed loss-of-function phenotypes. The majority of the substitutions affected citrate binding and translocation. The S75 residue had no impact on citrate export but affected its import, as the substitution for alanine increased the affinity of the transporter for citrate. Conversely, expression of CexA mutant alleles in the Yarrowia lipolytica cex1Δ strain revealed the involvement of R192 and Q196 residues in citrate export. Globally, we uncovered a set of relevant amino acid residues involved in CexA expression, export capacity and import affinity.

High-yield production of single-cell protein from starch processing wastewater using co-cultivation of yeasts

Single-cell protein (SCP) from potato starch processing wastewater (PSPW) shows great potential against protein scarcity and unsustainable production of plant and animal proteins. In this study, five yeasts were selected to conduct a series of PSPW fermentation for obtaining high-value SCP by optimizing fermentation conditions. The yeast combination was optimized as Candida utilis, Geotrichum candidum and Candida tropicalis with the volume proportion of 9:5:1. The inoculum size, temperature, rotation speed and initial pH were optimized at 12 %, 24℃, 200 r·min^-1 and ∼ 4.13 (natural pH), respectively. At the optimal conditions, SCP yield of 3.06 g·L^-1 and water-soluble protein of 17.32 % were obtained with the chemical oxygen demand removal of 56.9 %. A resource-recycling process of PSPW was proposed by coupling yeast fermentation and up-flow anaerobic sludge blanket (UASB) treatment to achieve simultaneous high-level organic removal and SCP production, which could be a promising alternative technology for PSPW treatment.

Enhanced production of 3,4-dihydroxybutyrate from xylose by engineered yeast via xylonate re-assimilation under alkaline condition

To realize lignocellulose-based bioeconomy, efficient conversion of xylose into valuable chemicals by microbes is necessary. Xylose oxidative pathways that oxidize xylose into xylonate can be more advantageous than conventional xylose assimilation pathways because of fewer reaction steps without loss of carbon and ATP. Moreover, commodity chemicals like 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone can be produced from the intermediates of xylose oxidative pathway. However, successful implementations of xylose oxidative pathway in yeast have been hindered because of the secretion and accumulation of xylonate which is a key intermediate of the pathway, leading to low yield of target product. Here, high-yield production of 3,4-dihydroxybutyrate from xylose by engineered yeast was achieved through genetic and environmental perturbations. Specifically, 3,4-dihydroxybutyrate biosynthetic pathway was established in yeast through deletion of ADH6 and overexpression of yneI. Also, inspired by the mismatch of pH between host strain and key enzyme of XylD, alkaline fermentations (pH ≥ 7.0) were performed to minimize xylonate accumulation. Under the alkaline conditions, xylonate was re-assimilated by engineered yeast and combined product yields of 3,4-dihydroxybutyrate and 3-hydroxybutyrolactone resulted in 0.791 mol/mol-xylose, which is highest compared with previous study. These results shed light on the utility of the xylose oxidative pathway in yeast.

Amperometric microbial biosensor for sugars and sweetener classification using principal component analysis in beverages

Sugar and artificial sweeteners are additives in packaged food and beverage products that are widely used, where excessive sugar consumption can cause an increase in various diseases. Detection and classification of natural sugars sucrose, fructose, glucose, and artificial sweetener aspartame are needed to determine the effects of consuming these sweeteners. This study uses an amperometric biosensor integrated biochip-D, which uses Saccharomyces cerevisiae as a bioreceptor through cellular metabolic respiration activity expressed in dissolved oxygen (DO) levels. The variations of sweetener concentration used were in the range of 50 mM to 250 mM. The measurement results showed that the higher the concentration of sugar and artificial sweeteners, the lower DO levels would be measured. It was due to the yeast cell respiration in consuming oxygen (O2) and producing carbon dioxide (CO2), where the decrease in DO levels of sucrose was 14.24%, fructose was 18.02%, glucose was 16.59%, and aspartame was 20.45% at a concentration of 250 mM. The measurement data was clustered and classified using principal component analysis (PCA), which resulted in data variance percentages of 92.80% and 89.40% for the two main components. In the application studies of the biosensor, sensitive determination of sugar in the beverage samples was investigated.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05625-8.

Suitability of select media for use in a novel green wall system used to treat brewery wastewater

Green walls are becoming increasingly popular as pleasing architectural installations and functional systems in sustainable urban building designs. However, utilization of green walls as an aqueous treatment option has been primarily limited to grey water. This study evaluates select media as appropriate support for plants and microorganisms in a novel green wall system used to treat wastewater from craft and micro-breweries. The media must have hydraulic capacity to treat large volumes of brewery wastewater, be lightweight and commercially available, and provide structure for plant roots and biofilm development. Two expanded recycled glass aggregates (Growstone^® and Poraver^®) and a lightweight expanded clay aggregate (Hydroton^®) were evaluated, having a d₅₀ range from 6 to 12 mm. To assess media performance, this study determined hydraulic characteristics and evaluated the growth of leafy green plants and microorganism populations irrigated with 100% raw brewery wastewater. It was determined that media with a particle d₅₀= 12 mm would facilitate a hydraulic loading rate of 1623 m³/m²/day media under unsaturated conditions and not result in interstitial velocities that shear away biofilm. No significant difference in plant growth metrics, microorganism type or cell density were observed between media. There were nearly three orders of magnitude more bacteria colonies than yeast CFU in biofilm. This innovative application of green walls has the potential to provide manufacturers of fermented beverages with a treatment option that has a low capital cost, simple to operate, and a small footprint, thereby avoiding traditional treatment processes and/or high sewer use fees.

Purification and characterization of a Metschnikowia pulcherrima killer toxin with antagonistic activity against pathogenic microorganisms

Yeasts can produce toxins in protein or glycoprotein structures that can act as an inhibitor on some bacteria and yeast species. The effects of those toxins on the growth of pathogenic and food spoilage microorganisms are subject to various studies. Metschnikowia pulcherrima was determined to be a killer toxin-producing yeast that was tested against three selected microorganisms, namely Escherichia coli Type-I, Micrococcus luteus and Candida albicans. The killer toxin only showed inhibitory activity against M. luteus. Different pH (5-6-7-8), temperature (20-25-30-35 °C) and carbon source (glucose-glycerol-ethanol-acetate) combinations were applied to stimulate the growth and toxin production of the killer yeast. The greatest increase among the different combinations was obtained at 20 °C and pH 7 when glycerol was used as the main carbon source. It was then also tested against other pathogen indicators or pathogens under these conditions. The killer toxin was partially purified by ethanol precipitation and showed inhibitory activity against M. luteus (36 mm). According to the protein profile obtained by SDS-PAGE, the molecular weight of the inhibitor toxin was measured about 7.4 kDa. The molecular weight with amino acid sequence of the killer toxin was 10.3 kDa and determined by MALDI-TOF mass spectrometry.

Xylose and yeasts: A story beyond xylitol production

Six different yeasts were used to study their metabolism of glucose and xylose, and mainly their capacity to produce ethanol and xylitol. The strains used were Candida guilliermondii, Debaryomyces hansenii, Saccharomyces cerevisiae, Kluyveromyces marxianus, Meyerozyma guilliermondii and Clavispora lusitaniae, four isolated from a rural mezcal fermentation facility. All of them produced ethanol when the substrate was glucose. When incubated in a medium containing xylose instead of glucose, only K. marxianus and M. guilliermondii were able to produce ethanol from xylose. On the other hand, all of them could produce some xylitol from xylose, but the most active in this regard were K. marxianus, M. guilliermondii, Candida lusitaniae, and C. guilliermondii with the highest amount of xylitol produced. The capacity of all strains to take up glucose and xylose was also studied. Xylose, in different degrees, produced a redox imbalance in all yeasts. Respiration capacity was also studied with glucose or xylose, where C. guilliermondii, D. hansenii, K. marxianus and M. guilliermondii showed higher cyanide resistant respiration when grown in xylose. Neither xylose transport nor xylitol production were enhanced by an acidic environment (pH 4), which can be interpreted as the absence of a proton/sugar symporter mechanism for xylose transport, except for C. lusitaniae. The effects produced by xylose and their magnitude depend on the background of the studied yeast and the conditions in which these are studied.

Physiological mechanisms by which gypsum increases the growth and yield of Lentinula edodes

Lentinula edodes is one of the most important commercially cultivated edible mushrooms. It is well known that gypsum (CaSO₄·2H₂O) supplementation in sawdust medium increases the yield of L. edodes, while the physiological mechanisms remain unclear. Our previous study showed that the acidification of the medium to pH 3.5-4.0 was essential for the growth of L. edodes. In this study, it was found that the oxalic acid excreted by L. edodes was responsible for the acidification of the medium. The biosynthesis of oxalic acid was regulated by the ambient pH and buffer capacity of the medium. To acidify the sawdust medium, the concentrations of total and soluble oxalate were 51.1 mmol/kg and 10.8 mmol/kg, respectively. However, when the concentration of soluble oxalate was 8.0 mmol/kg, the mycelial growth rate decreased by 29% compared with the control. Soluble oxalate was toxic to L. edodes, while soluble sulfate was nontoxic. CaSO₄ reacted with soluble oxalate to form nontoxic insoluble CaC₂O₄ and the strong acid H₂SO₄. When the CaSO₄ supplemented in sawdust medium was more than 25 mmol/kg, the soluble oxalate decreased to less than 1 mmol/kg, and the mycelial growth rate increased by 32% compared with the control. In conclusion, gypsum improved the growth and yield by relieving the toxicity of oxalate and facilitating the acidification of sawdust medium. KEY POINTS: • L. edodes excretes oxalic acid to acidify the ambient environment for growth. • Soluble oxalate is toxic to L. edodes. • Gypsum increases growth by reacting with oxalate to relieve its toxicity.

The human bile salt sodium deoxycholate induces metabolic and cell envelope changes in Salmonella Typhi leading to bile resistance

Introduction. Salmonella enterica serovar Typhi (S. Typhi) is the etiological agent of typhoid fever. To establish an infection in the human host, this pathogen must survive the presence of bile salts in the gut and gallbladder.Hypothesis. S. Typhi uses multiple genetic elements to resist the presence of human bile.Aims. To determine the genetic elements that S. Typhi utilizes to tolerate the human bile salt sodium deoxycholate.Methodology. A collection of S. Typhi mutant strains was evaluated for their ability to growth in the presence of sodium deoxycholate and ox-bile. Additionally, transcriptomic and proteomic responses elicited by sodium deoxycholate on S. Typhi cultures were also analysed.Results. Multiple transcriptional factors and some of their dependent genes involved in central metabolism, as well as in cell envelope, are required for deoxycholate resistance.Conclusion. These findings suggest that metabolic adaptation to bile is focused on enhancing energy production to sustain synthesis of cell envelope components exposed to damage by bile salts.

Modelling of fermentative bioethanol production from indigenous Ulva prolifera biomass by Saccharomyces cerevisiae NFCCI1248 using an integrated ANN-GA approach

Third generation biomass (marine macroalgae) has been projected as a promising alternative energy resource for bioethanol production due to its high carbon and no lignin composition. However, the major challenge in the technologies of production lies in the fermentative bioconversion process. Therefore, in the present study the predictive ability of an integrated artificial neural network with genetic algorithm (ANN-GA) in the modelling of bioethanol production was investigated for an indigenous marine macroalgal biomass (Ulva prolifera) by a novel yeast strain, Saccharomyces cerevisiae NFCCI1248 using six fermentative parameters, viz., substrate concentration, fermentation time, inoculum size, temperature, agitation speed and pH. The experimental model was developed using one-variable-at-a-time (OVAT) method to analyze the effects of the fermentative parameters on bioethanol production and the obtained regression equation was used as a fitness function for the ANN-GA modelling. The ANN-GA model predicted a maximum bioethanol production at 30 g/L substrate, 48 h fermentation time, 10% (v/v) inoculum, 30 °C temperature, 50 rpm agitation speed and pH 6. The maximum experimental bioethanol yield obtained after applying ANN-GA was 0.242 ± 0.002 g/g RS, which was in close proximity with the predicted value (0.239 g/g RS). Hence, the developed ANN-GA model can be applied as an efficient approach for predicting the fermentative bioethanol production from macroalgal biomass.

Mycoremediation of azo dyes using Cyberlindnera fabianii yeast strain: Application of designs of experiments for decolorization optimization

This study investigated the dye decolorization capacity of three yeast strains. Cyberlindnera fabianii was shortlisted for its high decolorization capacity and was further tested on various azo dyes. Based on the color of the biomass, and the UV-Vis analysis, Acid Red 14 was selected as a model dye, to examine the enzymatic biodegradation. The results showed significant increase in the intracellular and extracellular activities of laccase, tyrosinase, manganese peroxidase, and azoreductase. Phytotoxicity assessment indicated that the AR14 biodegradation by-products were not phytotoxic compared to the original dye molecules. Regarding the decolorization optimization, the screening of factors using the Plackett-Burman design showed that pH, dye concentration, and shaking speed had significant effects. These factors and their combined effect were evaluated using response surface methodology with the Box-Behnken model. The pH was the most significant factor, followed by dye concentration. The analysis of the contour plot and the 3D response surface diagram showed that the decolorization was inversely proportional to the increase in the initial dye concentration, but proportional to the initial pH and shaking speed. At optimal conditions (pH = 5.154, AR14 = 50 mg/L), C. fabianii could decolorize more than 97% of AR14 within 12 hr. PRACTITIONER POINTS: Cyberlindnera fabianii is a successful candidate for dye mycoremediation. Oxidase and reductase are the key enzymes involved in the biodegradation of azo dyes. By-products of Acid red 14 biodegradation are not phytoxic compared to the original dye. Design of experience tools enables to determine optimum conditions for efficient decolorization.

A buffered media system for yeast batch culture growth

Background

Fungi are premier hosts for the high-yield secretion of proteins for biomedical and industrial applications. The stability and activity of these secreted proteins is often dependent on the culture pH. As yeast acidifies the commonly used synthetic complete drop-out (SD) media that contains ammonium sulfate, the pH of the media needs to be buffered in order to maintain a desired extracellular pH during biomass production. At the same time, many buffering agents affect growth at the concentrations needed to support a stable pH. Although the standard for biotechnological research and development is shaken batch cultures or microtiter plate cultures that cannot be easily automatically pH-adjusted during growth, there is no comparative study that evaluates the buffering capacity and growth effects of different media types across pH-values in order to develop a pH-stable batch culture system.

Results

We systematically test the buffering capacity and growth effects of a citrate-phosphate buffer (CPB) from acidic to neutral pH across different media types. These media types differ in their nitrogen source (ammonium sulfate, urea or both). We find that the widely used synthetic drop-out media that uses ammonium sulfate as nitrogen source can only be effectively buffered at buffer concentrations that also affect growth. At lower concentrations, yeast biomass production still acidifies the media. When replacing the ammonium sulfate with urea, the media alkalizes. We then develop a medium combining ammonium sulfate and urea which can be buffered at low CPB concentrations that do not affect growth. In addition, we show that a buffer based on Tris/HCl is not effective in maintaining any of our media types at neutral pH even at relatively high concentrations.

Conclusion

Here we show that the buffering of yeast batch cultures is not straight-forward and addition of a buffering agent to set a desired starting pH does not guarantee pH-maintenance during growth. In response, we present a buffered media system based on an ammonium sulfate/urea medium that enables relatively stable pH-maintenance across a wide pH-range without affecting growth. This buffering system is useful for protein-secretion-screenings, antifungal activity assays, as well as for other pH-dependent basic biology or biotechnology projects.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02191-5.

Optimizing the biosynthesis of oxygenated and acetylated Taxol precursors in Saccharomyces cerevisiae using advanced bioprocessing strategies

Taxadien-5α-hydroxylase and taxadien-5α-ol O-acetyltransferase catalyze the oxidation of taxadiene to taxadien-5α-ol and subsequent acetylation to taxadien-5α-yl-acetate in the biosynthesis of the blockbuster anticancer drug, paclitaxel (Taxol®). Despite decades of research, the promiscuous and multispecific CYP725A4 enzyme remains a major bottleneck in microbial biosynthetic pathway development. In this study, an interdisciplinary approach was applied for the construction and optimization of the early pathway in Saccharomyces cerevisiae, across a range of bioreactor scales. High-throughput microscale optimization enhanced total oxygenated taxane titer to 39.0 ± 5.7 mg/L and total taxane product titers were comparable at micro and minibioreactor scale at 95.4 ± 18.0 and 98.9 mg/L, respectively. The introduction of pH control successfully mitigated a reduction of oxygenated taxane production, enhancing the potential taxadien-5α-ol isomer titer to 19.2 mg/L, comparable with the 23.8 ± 3.7 mg/L achieved at microscale. A combination of bioprocess optimization and increased gas chromatography-mass spectrometry resolution at 1 L bioreactor scale facilitated taxadien-5α-yl-acetate detection with a final titer of 3.7 mg/L. Total oxygenated taxane titers were improved 2.7-fold at this scale to 78 mg/L, the highest reported titer in yeast. Critical parameters affecting the productivity of the engineered strain were identified across a range of scales, providing a foundation for the development of robust integrated bioprocess control systems.

Study on the Inhibitory Activity of a Synthetic Defensin Derived from Barley Endosperm against Common Food Spoilage Yeast

In the food industry, food spoilage is a real issue that can lead to a significant amount of waste. Although current preservation techniques are being applied to reduce the occurrence of spoilage microorganisms, the problem persists. Food spoilage yeast are part of this dilemma, with common spoilers such as Zygosaccharomyces, Kluyveromyces, Debaryomyces and Saccharomyces frequently encountered. Antimicrobial peptides derived from plants have risen in popularity due to their ability to reduce spoilage. This study examines the potential application of a synthetic defensin peptide derived from barley endosperm. Its inhibitory effect against common spoilage yeasts, its mechanisms of action (membrane permeabilisation and overproduction of reactive oxygen species), and its stability in different conditions were characterised. The safety of the peptide was evaluated through a haemolysis and cytotoxicity assay, and no adverse effects were found. Both assays were performed to understand the effect of the peptide if it were to be consumed. Its ability to be degraded by a digestive enzyme was also examined for its safety. Finally, the peptide was successfully applied to different beverages and maintained the same inhibitory effects in apple juice as was observed in the antiyeast assays, providing further support for its application in food preservation.

Converting tequila vinasse diluted with tequila process water into microalgae-yeast flocs and dischargeable effluent

During tequila production from agave, wastewaters are produced, such as dark-colored vinasse. To add value to this vinasse, microalgae-yeast biomass was produced on vinasse diluted with tequila process water (first rinsing water of agave syrup production). In batch experiments, a vinasse concentration of 10 %v/v resulted in the highest biomass productivity, pH and microalgae growth compared to 20 and 30 %v/v. To ease harvesting, microalgae-yeast flocs (MaY-flocs) were developed in a sequencing batch reactor (SBR). A MaY-floc SBR was run with diluted vinasse (10 %v/v) enriched to 76 mg N-TA L^-1, resulting in a doubled biomass productivity (49.5 ± 8.3 mg VSS L^-1 day^-1) of MaY-flocs compared to the best batch reactor performance. Based on response surface experiments, enrichment to 150 mg N-TA L^-1 and 5.9 %v/v vinasse are recommended. The MaY-floc SBR system is a promising, novel technology to treat tequila wastewaters while producing settleable MaY-floc biomass of interest to aquaculture.

NanoRefinery of carbonaceous nanomaterials: Complementing dairy manure gasification and their applications in cellular imaging and heavy metal sensing

This article describes an efficient method, combining chemical oxidation and acetone extraction, to produce carbonaceous nanomaterials from dairy manure biochar. The optical and mechanical properties are similar to methods previously reported carbonaceous nanomaterials from biomass. Our novel process cuts the processing time in half and drastically reduces the energy input required. The acetone extraction produced 10 fractions with dairy manure biochar-derived carbonaceous nanomaterials (DMB-CNs). The fraction with the carbonaceous nanomaterials, DMB-CN-E1, with highest fluorescence was selected for in-depth characterisation and for initial testing across a range of applications. DMB-CN-E1 was characterised using atomic force microscope, electrophoresis, and spectrophotometric methods. DMB-CN-E1 exhibited a lateral dimension between 11 and 28 nm, a negative charge, and excitation/emission maxima at 337/410 nm, respectively. The bioimaging potential of DMB-CN-E1 evidenced different locations and different interactions with the cellular models evaluated. DMB-CN-E1 was quenched by several heavy metal ions showing a future application of these materials in heavy metal ion detection and/or removal. The demonstrated capabilities in bioimaging and environmental sensing create the opportunity for generating added-value nanomaterials (NanoRefinery) from dairy manure biochar gasification and, thus, increasing the economic viability of gasification plants.

A common mechanism explains the induction of aerobic fermentation and adaptive antioxidant response in Phaffia rhodozyma

Background

Growth conditions that bring about stress on Phaffia rhodozyma cells encourage the synthesis of astaxanthin, an antioxidant carotenoid, which protects cells against oxidative damage. Using P. rhodozyma cultures performed with and without copper limitation, we examined the kinetics of astaxanthin synthesis along with the expression of asy, the key astaxanthin synthesis gene, as well as aox, which encodes an alternative oxidase protein.

Results

Copper deficiency had a detrimental effect on the rates of oxygen consumption and ethanol reassimilation at the diauxic shift. In contrast, copper deficiency prompted alcoholic fermentation under aerobic conditions and had a favorable effect on the astaxanthin content of cells, as well as on aox expression. Both cultures exhibited strong aox expression while consuming ethanol, but particularly when copper was absent.

Conclusion

We show that the induction of either astaxanthin production, aox expression, or aerobic fermentation exemplifies the crucial role that redox imbalance plays in triggering any of these phenomena. Based on our own results and data from others, we propose a mechanism that rationalizes the central role played by changes of respiratory activity, which lead to redox imbalances, in triggering both the short-term antioxidant response as well as fermentation in yeasts and other cell types.

Evaluation of Alkali-Pretreated Soybean Straw for Lignocellulosic Bioethanol Production

Soybean straw is a renewable resource in agricultural residues that can be used for lignocellulosic bioethanol production. To enhance enzymatic digestibility and fermentability, the biomass was prepared with an alkali-thermal pretreatment (sodium hydroxide, 121°C, 60 min). The delignification yield was 34.1~53%, in proportion to the amount of sodium hydroxide, from 0.5 to 3.0 M. The lignin and hemicellulose contents of the pretreated biomass were reduced by the pretreatment process, whereas the proportion of cellulose was increased. Under optimal condition, the pretreated biomass consisted of 74.0±0.1% cellulose, 10.3±0.1% hemicellulose, and 10.1±0.6% lignin. During enzymatic saccharification using Cellic® CTec2 cellulase, 10% (w/v) of pretreated soybean straw was hydrolyzed completely and converted to 67.3±2.1 g/L glucose and 9.4±0.5 g/L xylose with a 90.9% yield efficiency. Simultaneous saccharification and fermentation of the pretreated biomass by Saccharomyces cerevisiae W303-1A produced 30.5±1.2 g/L ethanol in 0.5 L fermented medium containing 10% (w/v) pretreated biomass after 72 h. The ethanol productivity was 0.305 g ethanol/g dry biomass and 0.45 g ethanol/g glucose after fermentation, with a low concentration of organic acid metabolites. Also, 82% of fermentable sugar was used by the yeast for ethanol fermentation. These results show that the combination of alkaline pretreatment and biomass hydrolysate is useful for enhancing bioethanol productivity using delignified soybean straw.

Ratiometric fluorescent pH-sensitive polymers for high-throughput monitoring of extracellular pH

Extracellular pH has a strong effect on cell metabolism and growth. Precisely detecting extracellular pH with high throughput is critical for cell metabolism research and fermentation applications. In this research, a series of ratiometric fluorescent pH sensitive polymers are developed and the ps-pH-neutral is characterized as the best one for exculsive detection of extracellular pH. Poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA) is used as the host polymer to increase the water solubility of the pH sensitive polymer without introducing cell toxicity. The fluorescent emission spectra from the polymeric sensor under excitation at the isosbestic point 455 nm possess two fluorescence peaks at 475 nm and 505 nm, which have different responding trends to pH. This enables the polymer to detect pH using fluorescent maxima at 475 nm and 505 nm (I475nm /I505nm ) ratiometrically. The cell impermeability ensures the sensor can solely detect the environmental pH. The sensor is tested to detect the extracellular pH of bacteria or eukaryotic cells in high throughput assays using a microplate reader. Results showed that the pH sensor can be used for high throughput detection of extracellular pH with high repeatability and low photobleaching effect.

Whole-cell biocatalytic and de novo production of alkanes from free fatty acids in Saccharomyces cerevisiae

Rapid global industrialization in the past decades has led to extensive utilization of fossil fuels, which resulted in pressing environmental problems due to excessive carbon emission. This prompted increasing interest in developing advanced biofuels with higher energy density to substitute fossil fuels and bio‐alkane has gained attention as an ideal drop‐in fuel candidate. Production of alkanes in bacteria has been widely studied but studies on the utilization of the robust yeast host, Saccharomyces cerevisiae, for alkane biosynthesis have been lacking. In this proof‐of‐principle study, we present the unprecedented engineering of S. cerevisiae for conversion of free fatty acids to alkanes. A fatty acid α‐dioxygenase from Oryza sativa (rice) was expressed in S. cerevisiae to transform C_12–18 free fatty acids to C_11–17 aldehydes. Co‐expression of a cyanobacterial aldehyde deformylating oxygenase converted the aldehydes to the desired alkanes. We demonstrated the versatility of the pathway by performing whole‐cell biocatalytic conversion of exogenous free fatty acid feedstocks into alkanes as well as introducing the pathway into a free fatty acid overproducer for de novo production of alkanes from simple sugar. The results from this work are anticipated to advance the development of yeast hosts for alkane production. Biotechnol. Bioeng. 2017;114: 232–237. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.